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Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea.

Trantas EA, Licciardello G, Almeida NF, Witek K, Strano CP, Duxbury Z, Ververidis F, Goumas DE, Jones JD, Guttman DS, Catara V, Sarris PF - Front Microbiol (2015)

Bottom Line: This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison.Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains.Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

View Article: PubMed Central - PubMed

Affiliation: Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece.

ABSTRACT
The non-fluorescent pseudomonads, Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed), are closely related species that cause pith necrosis, a disease of tomato that causes severe crop losses. However, they also show strong antagonistic effects against economically important pathogens, demonstrating their potential for utilization as biological control agents. In addition, their metabolic versatility makes them attractive for the production of commercial biomolecules and bioremediation. An extensive comparative genomics study is required to dissect the mechanisms that Pcor and Pmed employ to cause disease, prevent disease caused by other pathogens, and to mine their genomes for genes that encode proteins involved in commercially important chemical pathways. Here, we present the draft genomes of nine Pcor and Pmed strains from different geographical locations. This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison. All examined strains were able to trigger symptoms in tomato plants but not all induced a hypersensitive-like response in Nicotiana benthamiana. Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains. The lack of a type III secretion system appears to be unique among the plant pathogenic pseudomonads. Several gene clusters coding for type VI secretion system were detected in all genomes. Genome-mining also revealed the presence of gene clusters for biosynthesis of siderophores, polyketides, non-ribosomal peptides, and hydrogen cyanide. A highly conserved quorum sensing system was detected in all strains, although species specific differences were observed. Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

No MeSH data available.


Related in: MedlinePlus

Distance tree of T6SSs of various pseudomonads based on the sequence of four T6SS core proteins (ImpC, ImpG, ImpH, and ImpL). The evolutionary history was inferred using the Neighbor-Joining method (Saitou and Nei, 1987). The bootstrap consensus tree inferred from 1500 replicates is taken to represent the evolutionary history of the proteins analyzed (Felsenstein, 1985). The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method (Zuckerkandl and Pauling, 1965) and are in theunits of the number of amino acid substitutions per site. The analysis involved 59 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 829 positions in the final dataset. Evolutionary analyses were conducted using MEGA6 (Tamura et al., 2013). “Pcor” stands for Pseudomonas corrugata while “Pmed” stands for P. mediterranea. “TEIC” strains came from the Technological Educational Institute of Crete Collection. CFBP strains came from the French Collection of Plant-associated Bacteria, part of the International Center for Microbial Resources.
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Figure 6: Distance tree of T6SSs of various pseudomonads based on the sequence of four T6SS core proteins (ImpC, ImpG, ImpH, and ImpL). The evolutionary history was inferred using the Neighbor-Joining method (Saitou and Nei, 1987). The bootstrap consensus tree inferred from 1500 replicates is taken to represent the evolutionary history of the proteins analyzed (Felsenstein, 1985). The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method (Zuckerkandl and Pauling, 1965) and are in theunits of the number of amino acid substitutions per site. The analysis involved 59 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 829 positions in the final dataset. Evolutionary analyses were conducted using MEGA6 (Tamura et al., 2013). “Pcor” stands for Pseudomonas corrugata while “Pmed” stands for P. mediterranea. “TEIC” strains came from the Technological Educational Institute of Crete Collection. CFBP strains came from the French Collection of Plant-associated Bacteria, part of the International Center for Microbial Resources.

Mentions: Phylogenetic analysis of various Pseudomonas species was performed using concatenated protein sequences of four highly conserved T6SS core proteins (ImpC, ImpG, ImpH, ImpL) (Figure 6). The consensus phylogenetic tree obtained indicates that pseudomonad T6SSs are scattered into three main clusters (Figure 6), and this matches what has been previously shown (Sarris et al., 2012).


Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea.

Trantas EA, Licciardello G, Almeida NF, Witek K, Strano CP, Duxbury Z, Ververidis F, Goumas DE, Jones JD, Guttman DS, Catara V, Sarris PF - Front Microbiol (2015)

Distance tree of T6SSs of various pseudomonads based on the sequence of four T6SS core proteins (ImpC, ImpG, ImpH, and ImpL). The evolutionary history was inferred using the Neighbor-Joining method (Saitou and Nei, 1987). The bootstrap consensus tree inferred from 1500 replicates is taken to represent the evolutionary history of the proteins analyzed (Felsenstein, 1985). The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method (Zuckerkandl and Pauling, 1965) and are in theunits of the number of amino acid substitutions per site. The analysis involved 59 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 829 positions in the final dataset. Evolutionary analyses were conducted using MEGA6 (Tamura et al., 2013). “Pcor” stands for Pseudomonas corrugata while “Pmed” stands for P. mediterranea. “TEIC” strains came from the Technological Educational Institute of Crete Collection. CFBP strains came from the French Collection of Plant-associated Bacteria, part of the International Center for Microbial Resources.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528175&req=5

Figure 6: Distance tree of T6SSs of various pseudomonads based on the sequence of four T6SS core proteins (ImpC, ImpG, ImpH, and ImpL). The evolutionary history was inferred using the Neighbor-Joining method (Saitou and Nei, 1987). The bootstrap consensus tree inferred from 1500 replicates is taken to represent the evolutionary history of the proteins analyzed (Felsenstein, 1985). The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method (Zuckerkandl and Pauling, 1965) and are in theunits of the number of amino acid substitutions per site. The analysis involved 59 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 829 positions in the final dataset. Evolutionary analyses were conducted using MEGA6 (Tamura et al., 2013). “Pcor” stands for Pseudomonas corrugata while “Pmed” stands for P. mediterranea. “TEIC” strains came from the Technological Educational Institute of Crete Collection. CFBP strains came from the French Collection of Plant-associated Bacteria, part of the International Center for Microbial Resources.
Mentions: Phylogenetic analysis of various Pseudomonas species was performed using concatenated protein sequences of four highly conserved T6SS core proteins (ImpC, ImpG, ImpH, ImpL) (Figure 6). The consensus phylogenetic tree obtained indicates that pseudomonad T6SSs are scattered into three main clusters (Figure 6), and this matches what has been previously shown (Sarris et al., 2012).

Bottom Line: This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison.Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains.Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

View Article: PubMed Central - PubMed

Affiliation: Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece.

ABSTRACT
The non-fluorescent pseudomonads, Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed), are closely related species that cause pith necrosis, a disease of tomato that causes severe crop losses. However, they also show strong antagonistic effects against economically important pathogens, demonstrating their potential for utilization as biological control agents. In addition, their metabolic versatility makes them attractive for the production of commercial biomolecules and bioremediation. An extensive comparative genomics study is required to dissect the mechanisms that Pcor and Pmed employ to cause disease, prevent disease caused by other pathogens, and to mine their genomes for genes that encode proteins involved in commercially important chemical pathways. Here, we present the draft genomes of nine Pcor and Pmed strains from different geographical locations. This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison. All examined strains were able to trigger symptoms in tomato plants but not all induced a hypersensitive-like response in Nicotiana benthamiana. Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains. The lack of a type III secretion system appears to be unique among the plant pathogenic pseudomonads. Several gene clusters coding for type VI secretion system were detected in all genomes. Genome-mining also revealed the presence of gene clusters for biosynthesis of siderophores, polyketides, non-ribosomal peptides, and hydrogen cyanide. A highly conserved quorum sensing system was detected in all strains, although species specific differences were observed. Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

No MeSH data available.


Related in: MedlinePlus